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Table 2 GEE, FBAT, and linkage results

From: Framingham Heart Study genome-wide association: results for pulmonary function measures

2a Top Association results based on GEE p-value

Phenotype

SNP

Chr

Physical position

GEE p-value

FBAT p-value

Gene Region

fev1slope

1. rs3867498

15

22629880

1.36 × 10 -06

0.07

SNRPN

meanfvc

2. rs441051

7

93698651

2.16 × 10 -06

0.005

COL1A2

meanratio

3. rs2838815

21

45454018

2.63 × 10 -06

0.0002

ADARB1

ppfvc

4. rs1455782

15

90851970

4.23 × 10 -06

0.18

FLJ32831

meanfvc

5. rs10516541

4

108472826

4.32 × 10 -06

7.19 × 10-05

 

meanfev1

   

1.7 × 10 -05

0.0002

 

ppratio

6. rs310558

8

51575144

5.14 × 10 -06

0.14

SNTG1

ppfev1

7. rs3820928

2

227598971

5.33 × 10 -06

0.0005

RHBDD1

ppfef

8. rs730532

14

51588561

5.89 × 10 -06

0.15

NID2

ppfefrat

9. rs808225

14

57467669

7.38 × 10 -06

0.0008

 

ppratio

   

1.45 × 10 -05

0.007

 

ppfef

10. rs4129267

1

151239337

7.39 × 10 -06

0.07

IL6R

ppfev1

11. rs2906966*

17

15272242

8.31 × 10 -06

5.03 × 10-05

CDRT4

ppfvc

12. rs357394

7

137506642

8.77 × 10 -06

0.14

 

fefslope

13. rs1994169

12

33436783

9.55 × 10 -06

0.05

SYT10

meanratio

14. rs2225434

21

45458574

9.68 × 10 -06

0.0004

ADARB1

meanfvc

15. rs156697(a)

10

106029175

9.78 × 10 -06

9.42 × 10-05

GSTO2

meanfev1

   

1.8 × 10 -05

0.002

 

ppfefrat

16. rs564425

13

46797096

1.03 × 10 -05

0.02

 

ppfef

17. rs10498441

14

51613974

1.06 × 10 -05

0.28

NID2

ppratio

18. rs880713

2

128847844

1.11 × 10 -05

0.26

AK128224

ppfefrat

19. rs811732

14

57456738

1.3 × 10 -05

0.20

 

ppfvc

20. rs6558132

8

29526866

1.58 × 10 -05

0.74

 

fev1slope

21. rs6972823

7

3009137

1.69 × 10 -05

0.10

 

ppfef

22. rs9285611(b)

1

81895076

1.7 × 10 -05

0.07

 

meanfev1

23. rs10504836

8

88669709

1.72 × 10 -05

0.28

 

meanfev1

24. rs1491520

3

193243153

1.77 × 10 -05

0.12

 

ppfvc

25. rs9300826

13

103001176

1.79 × 10 -05

0.11

 

2b Top Association results based on FBAT p-value

Phenotype

SNP

Chr

Physical position

GEE p-value

FBAT p-value

Gene Region

ppratio

1. rs10922530

1

89139273

0.001

8.7 × 10 -07

CCBL2

ppfefrat

   

0.002

3.78 × 10 -06

 

ppfef

   

0.005

2.36 × 10 -05

 

ppfefrat

2. rs3753683

1

89139592

0.004

1.87 × 10 -06

CCBL2

ppratio

   

0.004

3.59 × 10 -06

 

ppfef

   

0.01

1.42 × 10 -05

 

ppratio

3. rs219349

14

59525168

0.01

6.15 × 10 -06

LRRC9

ppfefrat

   

0.04

4.91 × 10 -05

 

ppratio

4. rs219391

14

59554684

0.02

6.18 × 10 -06

LRRC9

ppratio

5. rs219326

14

59512943

0.02

8.51 × 10 -06

LRRC9

ppfefrat

   

0.06

3.74 × 10 -05

 

ppfefrat

6. rs1409149

1

89141170

0.005

9.12 × 10 -06

CCBL2

ppratio

   

0.005

1.08 × 10 -05

 

ppfef

   

0.01

5.14 × 10 -05

 

ppfvc

7. rs9299191

9

110944100

0.009

1.79 × 10 -05

 

meanfvc

8. rs10515289(c)

5

99315845

0.17

2.21 × 10 -05

 

ppfvc

9. rs10498137

2

222966943

0.05

2.23 × 10 -05

PAX3

ppfef

10. rs3858282

10

90424391

0.001

2.92 × 10 -05

LIPF

ppratio

11. rs905367

4

59896363

0.02

2.95 × 10 -05

 

meanfvc

12. rs10495872

2

37915266

0.05

3.02 × 10 -05

 

fev1slope

13. rs1347222

12

80896622

0.01

3.27 × 10 -05

 

ppratio

14. rs2009488

4

59895895

0.03

3.43 × 10 -05

 

meanfvc

15. rs6481257

10

58608558

0.02

3.52 × 10 -05

 

ppratio

16. rs461951

14

59608986

0.02

3.63 × 10 -05

LRRC9

meanfev1

17. rs491552

6

151403169

0.01

3.86 × 10 -05

MTHFD1L

meanfev1

18. rs1910137

4

27087329

0.08

4.04 × 10 -05

 

ppfvc

19. rs2831605(d)

21

28467064

0.03

4.41 × 10 -05

 

ppfev1

20. rs2906966*

17

15272242

8.31 × 10-06

5.03 × 10 -05

CDRT4

fefslope

21. rs6740919

2

67531706

0.0009

5.17 × 10 -05

ETAA16

meanfev1

22. rs10498818

6

63134129

0.02

5.25 × 10 -05

 

ppfefrat

23. rs1393593

4

59907689

0.06

5.44 × 10 -05

 

ppfefrat

24. rs9312080

4

59891451

0.11

5.63 × 10 -05

 

ppfefrat

25. rs7851363

9

20748306

0.006

5.7 × 10 -05

KIAA1797

2c Linkage peaks with LOD score > 2.0

Phenotype

SNP

Chr

Physical position

1.5-LOD interval start

1.5-LOD interval end

LOD score

meanfev1

rs2300081

6

168097526

165513097

170788550

2.89

fefslope

rs5909594

X(e)

118057198

113970434

124311695

2.86

ppfev1

AGC001b

6

170788550

164268152

170788550

2.65

ppratio

rs10497042

2

150675813

148296793

154203261

2.40

meanratio

rs10518669

1

82811739

74999965

88728520(b)

2.37

ppfef

rs2974490

5

113433775

95608129

124687730(c)

2.29

meanfvc

rs10488908

21

21904704

19805361

34461762(d)

2.29

ppfev1

rs10518032

4

170322764

161768472

181501690

2.28

ppfvc

rs10489542

1

225169260

213625196

233478438

2.17

ppfef

rs721411

17

36902470

28313357

52519635

2.17

ppfev1

rs753765

17

57323782

45345729

59677087

2.17

meanfev1

rs4918762

10

114389096

102080914

122214789(a)

2.12

ppfvc

rs10517825

4

166251091

156507719

191091333

2.02

  1. *) SNP occurring in both Table 2a and 2b
  2. a) SNP associated to meanfvc and meanfev1 in Table 2a under linkage peak for meanfev1 on chromosome 10.
  3. b) SNP associated to ppfef in Table 2a under linkage peak for meanratio on chromosome 1.
  4. c) SNP associated to meanfvc in Table 2b under linkage peak for ppfef on chromosome 5.
  5. d) SNP associated to ppfvc in Table 2b under linkage peak for meanfvc on chromosome 21.
  6. e) X chromosome linkage results are not available online